Molecular profiling of tumors
Inventors
Von Hoff, Daniel D. • Loesch, David M. • Alarcon, Arlet • Penny, Robert J. • Wright, Alan • McGinniss, Matthew J. • Bender, Ryan P. • Pawlowski, Traci
Assignees
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Publication Number
US-9389234-B2
Publication Date
2016-07-12
Expiration Date
Abstract
Provided herein are methods and systems of molecular profiling of diseases, such as cancer. In some embodiments, the molecular profiling can be used to identify treatments for a disease, such as treatments that were not initially identified as a treatment for the disease or not expected to be a treatment for a particular disease.
Core Innovation
The invention provides a system for generating a report for an individual with cancer that identifies at least one therapeutic agent. The system includes at least one device configured to assay a plurality of molecular targets in a biological sample from the individual to determine molecular profile test values for the molecular targets.
The system further includes at least one computer database comprising a reference value for each molecular target and a listing of therapeutic agents with efficacy linked to a biological state of at least one member of the plurality of molecular targets. Computer-readable program code compares the molecular profile test values with the corresponding reference values to identify a biological state for each member of the plurality of molecular targets.
Computer-readable program code identifies at least one therapeutic agent from the listing of therapeutic agents, based on the biological state identified from the comparison to the reference values. The system generates a report that comprises a listing of the at least one therapeutic agent identified and the biological state of each molecular target with efficacy linked thereto. The molecular targets include ATRX, BRAF, CDH1, CDKN1B, CDKN2A, ERBB4, KRAS, MET, MYC, RAD51, and WISP3.
Claims Coverage
The independent claim is directed to a reporting system for selecting therapeutic agents based on assayed molecular targets and database-linked efficacy. Three inventive features are central: assaying molecular targets, matching test values to reference values to identify biological states, and generating a report linking therapeutic agents to those states.
Molecular profiling report-driven therapeutic agent identification
Assay molecular profile test values for a plurality of molecular targets in a biological sample, compare each molecular profile test value with a corresponding reference value to identify a biological state for each molecular target, and identify at least one therapeutic agent from a database listing therapeutic agents whose efficacy is linked to the biological state indicated by the comparison.
Reference-value and efficacy-linked database matching
Provide a computer database that includes a reference value for each molecular target and a listing of therapeutic agents with efficacy linked to a biological state of at least one member of the plurality of molecular targets.
Report generation linking therapeutic agents to biological states
Generate a report comprising a listing of the therapeutic agents identified and the biological state of each molecular target with efficacy linked thereto.
The claim coverage centers on comparing assayed molecular profile test values against database reference values to determine biological states, selecting therapeutic agents whose efficacy is linked to those states, and reporting the resulting agent-biological-state mappings.
Stated Advantages
Generates a report identifying at least one therapeutic agent for an individual with cancer based on likely benefit indicated by biological states linked to efficacy.
Produces a listing of therapeutic agents together with the biological state of each molecular target with efficacy linked thereto.
Provides an indication of likely benefit of at least one therapeutic agent for treating the cancer.
Supports inclusion of a listing of at least one additional therapeutic agent for which the biological state indicates likely lack of benefit.
Documented Applications
Biomarker-to-therapy linkage examples for cancer therapy selection using molecular profiling and reports, including HER2/neu (IHC/FISH) and PTEN status for recommending trastuzumab versus lapatinib; COX-2/aspirin survival associations; c-Kit mutation/exon status for stratifying imatinib versus sunitinib responses; and EGFR mutation/FISH/microarray with PTEN/KRAS/BRAF context for expected benefit or minimal benefit from EGFR-targeted therapies.
Personalized cancer therapy selection based on molecular profiling (IHC, FISH, microarray) and comparing outcomes using progression-free survival (PFS) and disease-free survival (DFS) ratios (e.g., PFS ratio ≥1.3) with supporting pilot study methodology and results.
Use of extensive system/clinical database and report-generation descriptions to generate patient profile reports.
For an individual with cancer, generate a report identifying at least one therapeutic agent using assayed molecular profile test values for molecular targets and database-linked efficacy.
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